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--
Ray Luo, Ph.D.
Professor
Biochemistry, Molecular Biophysics, Chemical Physics,
Chemical and Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Tue, Oct 18, 2016 at 2:21 PM, Vlad Cojocaru
<vlad.cojocaru.mpi-muenster.mpg.de> wrote:
> Hi Ray,
>
> Thanks for the report ...
>
> Curious ... Unfortunately, I cannot run Amber12 anymore to rerun our
> original calculations now but we do have significant differences between
> Amber12 (calculated back in 2013-2014) and Amber14 (calculated now)
> ....I will try to reinstall amber12 to see if I can confirm the
> differences ....
>
> Best,
> Vlad
>
>
>
> On 10/18/2016 07:47 PM, Ray Luo wrote:
>> Vlad,
>>
>> In my initial trial (using five snapshots, every 10000 frames) of all
>> three releases, amber12, amber14, and amber16, only amber16 gives
>> different EEL (i.e. EELEC + EPB). Indeed the differences between
>> amber16 and the other two releases are larger than what we saw in the
>> test cases. I'm turning on the verbal mode to see what is the cause.
>>
>> All the best,
>> Ray
>> --
>> Ray Luo, Ph.D.
>> Professor
>> Biochemistry, Molecular Biophysics, Chemical Physics,
>> Chemical and Biomedical Engineering
>> University of California, Irvine, CA 92697-3900
>>
>>
>> On Fri, Oct 14, 2016 at 11:29 AM, Ray Luo <rluo.uci.edu> wrote:
>>> Vlad,
>>>
>>> Looks like your input parameters are reasonably set. If you see much
>>> higher differences among different releases for your system, maybe you want
>>> to email your inpcrd/prmtop files to me OFF THE LIST so I can see
>>> what's the cause.
>>>
>>> All the best,
>>> Ray
>>> --
>>> Ray Luo, Ph.D.
>>> Professor
>>> Biochemistry, Molecular Biophysics, Chemical Physics,
>>> Chemical and Biomedical Engineering
>>> University of California, Irvine, CA 92697-3900
>>>
>>>
>>> On Fri, Oct 14, 2016 at 10:35 AM, Vlad Cojocaru
>>> <vlad.cojocaru.mpi-muenster.mpg.de> wrote:
>>>> Hi Ray,
>>>>
>>>> Now I don't have access to the computers but the differences I am seeing
>>>> in the deltaG are from -26 (amber12), to -40 (amber14), to -77 (amber16)
>>>> .... As the only difference in the outputs are in the EEL energy (all
>>>> other terms are identical), this is a change of 200% percent with each
>>>> Amber version ...
>>>>
>>>> But I will take a look again at the test cases on Monday and try to
>>>> rationalize further ...
>>>>
>>>> Its a little frustrating because I was quite happy with the values we
>>>> got using Amber 12 and now it turns out that simply changing the version
>>>> of the program we use, we get huge differences to our original results
>>>> ... Maybe the ddGs or dddGs we reported in the Structure paper 2014 are
>>>> unaffected (did not do a full test for that yet) but still it is
>>>> frustrating to see such differences by just changing the version of the
>>>> program .....
>>>>
>>>> Best
>>>> Vlad
>>>>
>>>> On 10/14/2016 06:34 PM, Ray Luo wrote:
>>>>> Hi Vlad,
>>>>>
>>>>> I found the reason of the discrepancy. If you look at the standard
>>>>> nonlinear PB test cases (under AmberTools/test/pbsa_npb), they are
>>>>> consistent between amber12 and amber14. While working on his NPB/P3M
>>>>> algorithm for the amber16 release, my student, Li Xiao, found a flip
>>>>> of sign in the bulk ion energy calculation. You can find his comment
>>>>> in routine pb_ionene() within "pb_nlsolver.F90". After his fix, we see
>>>>> a change about 0.7% in the total EELEC energies in our test cases.
>>>>> I'll confirm with him again regarding this.
>>>>>
>>>>> All the best,
>>>>> Ray
>>>>> --
>>>>> Ray Luo, Ph.D.
>>>>> Professor
>>>>> Biochemistry, Molecular Biophysics, Chemical Physics,
>>>>> Chemical and Biomedical Engineering
>>>>> University of California, Irvine, CA 92697-3900
>>>>>
>>>>>
>>>>> On Fri, Oct 14, 2016 at 8:44 AM, Ray Luo <rluo.uci.edu> wrote:
>>>>>> Vlad,
>>>>>>
>>>>>> As for the P3M approach, you probably don't want to freely adjust the
>>>>>> cutoff distance because the nonbonded list is shared between direct
>>>>>> pairwise sum and surface generation routines.
>>>>>>
>>>>>> I'm looking at your input files right now. In general, we have mostly
>>>>>> focussed on the default setup that is used by most users to ensure
>>>>>> consistency between releases. Other rarely used options are not tested
>>>>>> often. Maybe we should put your test into the release test cases so we
>>>>>> can check it every time the code is changed. What do you think?
>>>>>>
>>>>>> All the best,
>>>>>> Ray
>>>>>> --
>>>>>> Ray Luo, Ph.D.
>>>>>> Professor
>>>>>> Biochemistry, Molecular Biophysics, Chemical Physics,
>>>>>> Chemical and Biomedical Engineering
>>>>>> University of California, Irvine, CA 92697-3900
>>>>>>
>>>>>>
>>>>>> On Fri, Oct 14, 2016 at 1:42 AM, Vlad Cojocaru
>>>>>> <vlad.cojocaru.mpi-muenster.mpg.de> wrote:
>>>>>>> Thanks ...
>>>>>>>
>>>>>>> Sorry, I need to ask another question ... I am now playing with lots of
>>>>>>> parameters and in one run I set cutnb to a higher value (with eneopt =
>>>>>>> 4) but I get an error that points me to a "cutres" option which I could
>>>>>>> not find in the manual.
>>>>>>>
>>>>>>> Could you please let me know me what the "cutres" option is ?
>>>>>>>
>>>>>>> Thanks
>>>>>>> Vlad
>>>>>>>
>>>>>>> On 10/14/2016 12:23 AM, Ray Luo wrote:
>>>>>>>> I'm teaching this quarter and haven't got a time to look at your
>>>>>>>> files, but I'll look at your example next ...
>>>>>>>>
>>>>>>>> It's most likely due to the different default optimal values and/or
>>>>>>>> bug fixes ... I will run your jobs without specifying any parameters
>>>>>>>> first to see whether the default behaviors are similar. This is how
>>>>>>>> new releases were first tested against previous versions. When you
>>>>>>>> specify most not not all parameters explicitly, the default behaviors
>>>>>>>> would get changed somewhat.
>>>>>>>>
>>>>>>>> As for speedup in Amber16, yes, this is due to a major code cleanup to
>>>>>>>> organize the modules better.
>>>>>>>>
>>>>>>>> All the best,
>>>>>>>> Ray
>>>>>>>> --
>>>>>>>> Ray Luo, Ph.D.
>>>>>>>> Professor
>>>>>>>> Biochemistry, Molecular Biophysics, Chemical Physics,
>>>>>>>> Chemical and Biomedical Engineering
>>>>>>>> University of California, Irvine, CA 92697-3900
>>>>>>>>
>>>>>>>>
>>>>>>>> On Thu, Oct 13, 2016 at 8:43 AM, Vlad Cojocaru
>>>>>>>> <vlad.cojocaru.mpi-muenster.mpg.de> wrote:
>>>>>>>>> Dear Ray, Dear all,
>>>>>>>>>
>>>>>>>>> I also performed exactly the same calculation I described in my original
>>>>>>>>> mail with Amber 14 .. Every version of Amber provides different values for
>>>>>>>>> the electrostatic energies although the run was done with exactly the same
>>>>>>>>> scripts, on exactly same topologies and trajectory .. Moreover, almost all
>>>>>>>>> pbsa parameters are specified explicitly in the input MDIN file (see again
>>>>>>>>> original mail below) ...
>>>>>>>>>
>>>>>>>>> Best wishes
>>>>>>>>> Vlad
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 10/13/2016 10:47 AM, Vlad Cojocaru wrote:
>>>>>>>>>> Hi Ray,
>>>>>>>>>>
>>>>>>>>>> It would be great if we could understand where these differences come
>>>>>>>>>> from ...I looked at all parameters from my customized MDIN file (which I
>>>>>>>>>> attached to my original mail below) and I did not notice any change
>>>>>>>>>> between Amber 12 and Amber 16 in terms of the meaning of the values
>>>>>>>>>> (hope I did not miss anything). I am now doing the same calculation
>>>>>>>>>> with Amber 14 as well to see if the difference came between Amber 12 and
>>>>>>>>>> Amber 14 or between Amber 14 to Amber 16 ...
>>>>>>>>>>
>>>>>>>>>> On a side note, the calculation is much faster with Amber 16 comparing
>>>>>>>>>> to Amber 14 ... Is that to be expected ?
>>>>>>>>>>
>>>>>>>>>> Thanks for looking into this
>>>>>>>>>> Vlad
>>>>>>>>>>
>>>>>>>>>> On 10/12/2016 10:44 AM, Ray Luo wrote:
>>>>>>>>>>> Hi Vlad,
>>>>>>>>>>>
>>>>>>>>>>> Thanks a lot for letting us know! I suppose the default was changed in
>>>>>>>>>>> the script or the code. Will let you know the cause.
>>>>>>>>>>>
>>>>>>>>>>> All the best,
>>>>>>>>>>> Ray
>>>>>>>>>>> --
>>>>>>>>>>> Ray Luo, Ph.D.
>>>>>>>>>>> Professor
>>>>>>>>>>> Biochemistry, Molecular Biophysics, Chemical Physics,
>>>>>>>>>>> Chemical and Biomedical Engineering
>>>>>>>>>>> University of California, Irvine, CA 92697-3900
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Wed, Oct 12, 2016 at 1:31 AM, Vlad Cojocaru
>>>>>>>>>>> <vlad.cojocaru.mpi-muenster.mpg.de> wrote:
>>>>>>>>>>>> Dear all,
>>>>>>>>>>>>
>>>>>>>>>>>> I am trying to reproduce some of our previous MMPBSA calculations with
>>>>>>>>>>>> Amber
>>>>>>>>>>>> 16. Original calculations were done in Amber 12. Now, using exactly the
>>>>>>>>>>>> same
>>>>>>>>>>>> trajectory, exactly same topology files, exactly the same input files
>>>>>>>>>>>> (see
>>>>>>>>>>>> below the MMPBSA input as well as the customized MDIN), I get an
>>>>>>>>>>>> absolute
>>>>>>>>>>>> affinity (without entropy) of -77 kcal/mol versus previously calculated
>>>>>>>>>>>> -26
>>>>>>>>>>>> kcal/mol ... The only difference between the runs in actually in the
>>>>>>>>>>>> electrostatic energy (-43.5 in the new calculation versus +8 in the old
>>>>>>>>>>>> calculation) . See attached output files.
>>>>>>>>>>>>
>>>>>>>>>>>> Therefore, the problem (or difference) is in the PB solver in Amber 16
>>>>>>>>>>>> versus Amber 12 ... Does anybody have any idea where the difference
>>>>>>>>>>>> could
>>>>>>>>>>>> come from ??
>>>>>>>>>>>>
>>>>>>>>>>>> I know that one should not put too much weight on the absolute values,
>>>>>>>>>>>> but
>>>>>>>>>>>> still running with exactly the same scripts, exactly same topology
>>>>>>>>>>>> files,
>>>>>>>>>>>> exactly the same old trajectory in 2 different versions of the same
>>>>>>>>>>>> program
>>>>>>>>>>>> should give the same results ....
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks for any insights in this
>>>>>>>>>>>>
>>>>>>>>>>>> Best wishes
>>>>>>>>>>>> Vlad
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> ---- MMPBSA INPUT -----
>>>>>>>>>>>> MMPBSA
>>>>>>>>>>>> &general
>>>>>>>>>>>> debug_printlevel=1,
>>>>>>>>>>>> startframe=${startframe},
>>>>>>>>>>>> endframe=${endframe},
>>>>>>>>>>>> interval=${interval},
>>>>>>>>>>>> keep_files=1,
>>>>>>>>>>>> netcdf=1,
>>>>>>>>>>>> ligand_mask=":${r1_ligand}-${r2_ligand}",
>>>>>>>>>>>> receptor_mask=":${r1_receptor}-${r2_receptor}",
>>>>>>>>>>>> use_sander=1,
>>>>>>>>>>>> entropy=0,
>>>>>>>>>>>> full_traj=1,
>>>>>>>>>>>> verbose=2,
>>>>>>>>>>>> /
>>>>>>>>>>>> &pb
>>>>>>>>>>>> inp=2,
>>>>>>>>>>>> cavity_offset=-0.5692,
>>>>>>>>>>>> cavity_surften=0.0378,
>>>>>>>>>>>> indi=4.0,
>>>>>>>>>>>> exdi=80.0,
>>>>>>>>>>>> fillratio=4.0,
>>>>>>>>>>>> istrng=0.100,
>>>>>>>>>>>> linit=1000,
>>>>>>>>>>>> prbrad=1.4,
>>>>>>>>>>>> radiopt=1,
>>>>>>>>>>>> scale=2.0,
>>>>>>>>>>>> /
>>>>>>>>>>>>
>>>>>>>>>>>> $MPI_HOME/bin/mpirun -n $NSLOTS $AMBERHOME/bin/MMPBSA.py.MPI -O -i
>>>>>>>>>>>> mmpbsa_${run}.in \
>>>>>>>>>>>> -o
>>>>>>>>>>>> mmpbsa_${run}.out \
>>>>>>>>>>>> -cp
>>>>>>>>>>>> ${top_complex} \
>>>>>>>>>>>> -rp
>>>>>>>>>>>> ${top_receptor} \
>>>>>>>>>>>> -lp
>>>>>>>>>>>> ${top_ligand} \
>>>>>>>>>>>> -y
>>>>>>>>>>>> ${traj_complex} \
>>>>>>>>>>>> -eo
>>>>>>>>>>>> energy_${run}.out \
>>>>>>>>>>>> -use-mdins
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> ---- MDIN ------------------------
>>>>>>>>>>>> MMPBSA, Nonlinear PB, inp=2, sasopt=2
>>>>>>>>>>>> &cntrl
>>>>>>>>>>>> nsnb=99999, dec_verbose=0, ioutfm=1,
>>>>>>>>>>>> ipb=2, ntb=0, cut=999.0, imin=5,
>>>>>>>>>>>> igb=10, inp=2,
>>>>>>>>>>>> /
>>>>>>>>>>>> &pb
>>>>>>>>>>>> epsin=4, epsout=80, smoothopt=1,
>>>>>>>>>>>> istrng=100.0, pbtemp=300, radiopt=1,
>>>>>>>>>>>> dprob=1.4, iprob=2.0, sasopt=2, saopt=0,
>>>>>>>>>>>> triopt=1, arcres=0.25,
>>>>>>>>>>>> npbopt=1, solvopt=1, accept=0.001,
>>>>>>>>>>>> maxitn=100, fillratio=4.0, space=0.5,
>>>>>>>>>>>> nbuffer=0, nfocus=2, fscale=8, npbgrid=1,
>>>>>>>>>>>> bcopt=5, eneopt=1, frcopt=0, scalec=0,
>>>>>>>>>>>> cutfd=5.0, cutnb=12, nsnba=1,
>>>>>>>>>>>> phiout=0,
>>>>>>>>>>>> decompopt=2, use_rmin=1, sprob=0.557, vprob=1.3,
>>>>>>>>>>>> rhow_effect=1.129, use_sav=1,
>>>>>>>>>>>> cavity_surften=0.0378, cavity_offset=-0.5692,
>>>>>>>>>>>> maxsph=400,
>>>>>>>>>>>> /
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> --
>>>>>>>>>>>> Dr. Vlad Cojocaru
>>>>>>>>>>>> Computational Structural Biology Laboratory
>>>>>>>>>>>> Department of Cell and Developmental Biology
>>>>>>>>>>>> Max Planck Institute for Molecular Biomedicine
>>>>>>>>>>>> Röntgenstrasse 20, 48149 Münster, Germany
>>>>>>>>>>>> Tel: +49-251-70365-324; Fax: +49-251-70365-399
>>>>>>>>>>>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>>>>>>>>>>>> http://www.mpi-muenster.mpg.de/43241/cojocaru
>>>>>>>>>>>>
>>>>>>>>>>>>
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>>>>>>>>> --
>>>>>>>>> Dr. Vlad Cojocaru
>>>>>>>>> Computational Structural Biology Laboratory
>>>>>>>>> Department of Cell and Developmental Biology
>>>>>>>>> Max Planck Institute for Molecular Biomedicine
>>>>>>>>> Röntgenstrasse 20, 48149 Münster, Germany
>>>>>>>>> Tel: +49-251-70365-324; Fax: +49-251-70365-399
>>>>>>>>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>>>>>>>>> http://www.mpi-muenster.mpg.de/43241/cojocaru
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
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>>>>>>>>>
>>>>>>>> _______________________________________________
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>>>>>>> --
>>>>>>> Dr. Vlad Cojocaru
>>>>>>> Computational Structural Biology Laboratory
>>>>>>> Department of Cell and Developmental Biology
>>>>>>> Max Planck Institute for Molecular Biomedicine
>>>>>>> Röntgenstrasse 20, 48149 Münster, Germany
>>>>>>> Tel: +49-251-70365-324; Fax: +49-251-70365-399
>>>>>>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>>>>>>> http://www.mpi-muenster.mpg.de/43241/cojocaru
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> AMBER mailing list
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>>>> --
>>>> Dr. Vlad Cojocaru
>>>> Computational Structural Biology Laboratory
>>>> Department of Cell and Developmental Biology
>>>> Max Planck Institute for Molecular Biomedicine
>>>> Röntgenstrasse 20, 48149 Münster, Germany
>>>> Tel: +49-251-70365-324; Fax: +49-251-70365-399
>>>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>>>> http://www.mpi-muenster.mpg.de/43241/cojocaru
>>>>
>>>>
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>
> --
> Dr. Vlad Cojocaru
> Computational Structural Biology Laboratory
> Department of Cell and Developmental Biology
> Max Planck Institute for Molecular Biomedicine
> Röntgenstrasse 20, 48149 Münster, Germany
> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
> http://www.mpi-muenster.mpg.de/43241/cojocaru
>
>
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Received on Tue Oct 18 2016 - 16:30:03 PDT